diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index cde3b5df9a82347651848fc4c16da5fc175b8531..7f289416e511bbccef3acb5dd394980480cb553c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -3,8 +3,6 @@ pages: image: rocker/r-rmd script: - mkdir -p public/img - - ls -l - - pwd - make - cp 1_scrnaseq_data/scrnaseq_data.pdf 2_normalization/normalization.pdf 3_dimension_reduction/dimension_reduction.pdf 4_clustering/clustering.pdf 5_pseudo_time/pseudo_time.pdf 6_dea/dea.pdf public/ artifacts: diff --git a/1_scrnaseq_data/scrnaseq_data.Rmd b/1_scrnaseq_data/scrnaseq_data.Rmd index b2bbf4c52220a8628cf4cfb3d93ee6293dc4c5cf..766e43b7c1e27bea9563de7a3d7ab5b7fe42f3d0 100644 --- a/1_scrnaseq_data/scrnaseq_data.Rmd +++ b/1_scrnaseq_data/scrnaseq_data.Rmd @@ -789,8 +789,7 @@ Do we keep reads mapping after the annotated 3' UTR ? \begin{columns} \column{0.65\textwidth} \begin{center} -\includegraphics[width=\textwidth]{img/discared_reads.png -} +\includegraphics[width=\textwidth]{img/discared_reads.png} \end{center} \column{0.35\textwidth} {\bf Your best marker genes could be in the small percent of genes lost} @@ -803,8 +802,7 @@ Why bother ? \vspace{-1.5em} \begin{center} -\includegraphics[width=.8\textwidth]{img/full_length_vs_3prim.png -} +\includegraphics[width=.8\textwidth]{img/full_length_vs_3prim.png} \end{center} # Quantification diff --git a/5_pseudo_time/pseudo_time.Rmd b/5_pseudo_time/pseudo_time.Rmd index 178b511469a071cc2f452bdc4bd2f1198ecfd761..36b215b1ab9db226c93340e399d20fc25dd42cf0 100644 --- a/5_pseudo_time/pseudo_time.Rmd +++ b/5_pseudo_time/pseudo_time.Rmd @@ -369,25 +369,28 @@ When we have a scRNASeq time serie we want: ## Waddington OT +### Finding the best cell coupling \begin{center} \href{olivier gandrillon}{ - \includegraphics[width=0.5\textwidth]{img/coupling_1.png} + \includegraphics[width=0.4\textwidth]{img/coupling_1.png} } \end{center} ## Waddington OT +### Finding the best cell coupling \begin{center} \href{olivier gandrillon}{ - \includegraphics[width=0.5\textwidth]{img/coupling_2.png} + \includegraphics[width=0.4\textwidth]{img/coupling_2.png} } \end{center} ## Waddington OT +### Finding the best cell coupling \begin{center} \href{olivier gandrillon}{ - \includegraphics[width=0.5\textwidth]{img/coupling_3.png} + \includegraphics[width=0.4\textwidth]{img/coupling_3.png} } \end{center}